|
2
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_diversity_mantel" name="qiime diversity mantel" version="2019.4">
|
|
|
3 <description> - Apply the Mantel test to two distance matrices</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2019.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime diversity mantel
|
|
|
9
|
|
|
10 --i-dm1=$idm1
|
|
|
11 --i-dm2=$idm2
|
|
|
12
|
|
|
13 #if str($pmethod) != 'None':
|
|
|
14 --p-method=$pmethod
|
|
|
15 #end if
|
|
|
16
|
|
|
17 #if $ppermutations:
|
|
|
18 --p-permutations=$ppermutations
|
|
|
19 #end if
|
|
|
20
|
|
|
21 #if $pintersectids:
|
|
|
22 --p-intersect-ids
|
|
|
23 #end if
|
|
|
24
|
|
|
25 #if str($plabel1):
|
|
|
26 --p-label1="$plabel1"
|
|
|
27 #end if
|
|
|
28
|
|
|
29 #if str($plabel2):
|
|
|
30 --p-label2="$plabel2"
|
|
|
31 #end if
|
|
|
32
|
|
|
33 --o-visualization=ovisualization
|
|
|
34 ;
|
|
|
35 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
|
|
|
36 && cp -r out/* '$ovisualization.files_path'
|
|
|
37 && mv '$ovisualization.files_path/index.html' '$ovisualization';
|
|
|
38 ]]></command>
|
|
|
39 <inputs>
|
|
|
40 <param format="qza,no_unzip.zip" label="--i-dm1: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm1" optional="False" type="data"/>
|
|
|
41 <param format="qza,no_unzip.zip" label="--i-dm2: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm2" optional="False" type="data"/>
|
|
|
42 <param label="--p-method: " name="pmethod" optional="True" type="select">
|
|
|
43 <option selected="True" value="None">Selection is Optional</option>
|
|
|
44 <option value="spearman">spearman</option>
|
|
|
45 <option value="pearson">pearson</option>
|
|
|
46 </param>
|
|
|
47 <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/>
|
|
|
48 <param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean"/>
|
|
|
49 <param label="--p-label1: TEXT Label for `dm1` in the output visualization. [default: 'Distance Matrix 1']" name="plabel1" optional="True" type="text" value="'Distance Matrix 1'"/>
|
|
|
50 <param label="--p-label2: TEXT Label for `dm2` in the output visualization. [default: 'Distance Matrix 2']" name="plabel2" optional="True" type="text" value="'Distance Matrix 2'"/>
|
|
|
51 </inputs>
|
|
|
52 <outputs>
|
|
|
53 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
|
|
|
54 </outputs>
|
|
|
55 <help><![CDATA[
|
|
|
56 Apply the Mantel test to two distance matrices
|
|
|
57 ##############################################
|
|
|
58
|
|
|
59 Apply a two-sided Mantel test to identify correlation between two distance
|
|
|
60 matrices. Note: the directionality of the comparison has no bearing on the
|
|
|
61 results. Thus, comparing distance matrix X to distance matrix Y is
|
|
|
62 equivalent to comparing Y to X. Note: the order of samples within the two
|
|
|
63 distance matrices does not need to be the same; the distance matrices will
|
|
|
64 be reordered before applying the Mantel test. See the scikit-bio docs for
|
|
|
65 more details about the Mantel test: http://scikit-
|
|
|
66 bio.org/docs/latest/generated/generated/skbio.stats.distance.mantel.html
|
|
|
67
|
|
|
68 Parameters
|
|
|
69 ----------
|
|
|
70 dm1 : DistanceMatrix
|
|
|
71 Matrix of distances between pairs of samples.
|
|
|
72 dm2 : DistanceMatrix
|
|
|
73 Matrix of distances between pairs of samples.
|
|
|
74 method : Str % Choices('spearman', 'pearson'), optional
|
|
|
75 The correlation test to be applied in the Mantel test.
|
|
|
76 permutations : Int % Range(0, None), optional
|
|
|
77 The number of permutations to be run when computing p-values. Supplying
|
|
|
78 a value of zero will disable permutation testing and p-values will not
|
|
|
79 be calculated (this results in *much* quicker execution time if
|
|
|
80 p-values are not desired).
|
|
|
81 intersect_ids : Bool, optional
|
|
|
82 If supplied, IDs that are not found in both distance matrices will be
|
|
|
83 discarded before applying the Mantel test. Default behavior is to error
|
|
|
84 on any mismatched IDs.
|
|
|
85 label1 : Str, optional
|
|
|
86 Label for `dm1` in the output visualization.
|
|
|
87 label2 : Str, optional
|
|
|
88 Label for `dm2` in the output visualization.
|
|
|
89
|
|
|
90 Returns
|
|
|
91 -------
|
|
|
92 visualization : Visualization
|
|
|
93 ]]></help>
|
|
|
94 <macros>
|
|
|
95 <import>qiime_citation.xml</import>
|
|
|
96 </macros>
|
|
|
97 <expand macro="qiime_citation"/>
|
|
|
98 </tool>
|
